Nanopore capture system

ABSTRACT

A nanopore capture system may include a material configured to pass through a nanopore device in a controlled manner based upon its interaction with the nanopore device. The system may also include a capture mechanism connected to one end of the material. The capture mechanism may be configured to catch a particular type of molecule while ignoring other types of molecules. The system may also include a controller to manipulate and/or detect the particular type of molecule.

RELATED APPLICATIONS

This application contains subject matter related to the subject matterof a co-pending application entitled “Systems and Methods forControlling the Position of a Charged Polymer Inside a Nanopore” andhaving U.S. Publication No. 2008/0187915, the entire subject matter ofwhich is incorporated herein by reference in its entirety. Theaforementioned application is assigned to the same assignee as thisapplication, International Business Machines Corporation of Armonk, N.Y.

BACKGROUND

1. Field of the Invention

The invention relates to the field of nanopores, and, more particularly,to nanopore systems.

2. Description of Background

Generally, a nanopore is a hole of a predetermined size in a solidmaterial or a protein pore in a biological membrane. The nanopore isformed or fabricated in a solid material may be sized according to itsintended use. The nanopore may be, for example, drilled or etched intothe solid material.

Nanopore systems are being developed for use in sensing and controllingmolecules and/or bio-molecules. In such systems, the nanopore is usuallysized to have an inner diameter slightly larger than the outer diameterof the molecule being studied.

SUMMARY

An example embodiment of the present invention is a nanopore regulationsystem. The system may include a material configured to traverse ananopore opening in a solid state membrane device in a controlled mannerbased upon its interaction with the solid state membrane device. Thenanopore opening may be sized to limit the passage of a particularmolecule through it. The system further includes a capture mechanismconnected to one end of the material. The capture mechanism isconfigured to bond to a particular type of molecule while not bonding toother types of molecules.

The system may also include a first electrode adjacent one side of thenanopore opening, and a second electrode adjacent the other side of thenanopore opening. The first electrode and the second electrode may beconfigured to regulate the material's position with respect to thenanopore device. Moreover, the second electrode may interact with thefirst electrode to produce an electric field that regulates and monitorsthe passage of the particular molecule through the nanopore opening.

The material may include a polymer and/or a non-biological molecule. Thepolymer may comprise a polypeptide. The system may also include acontroller to detect the particular molecule and/or manipulate theparticular molecule's location. The controller may detect the particularmolecule based upon voltage changes in control electrodes and/or ioniccurrent changes.

The capture mechanism may include an antibody, a deoxyribonucleic acidbinding protein, a nucleic acid or peptide aptamer, an oligonucleotide,and/or nucleic acid fragments for complementary strand hybridization.The controller may process the particular molecule.

The controller may destroy the particular molecule. The system mayinclude a reservoir adjacent at least one side of the nanopore devicethat is flushed after the particular molecule is destroyed.

The system may include a first electrode adjacent one side of thenanopore device, and a second electrode adjacent the other side of thenanopore device.

Another example embodiment of the present invention is a nanoporecapture system method. The method may include connecting a capturemechanism to one end of a material, with the capture mechanismconfigured to catch a particular type of molecule while ignoring othertypes of molecules. The method may also include controlling the passageof the material through a nanopore device based upon the material'sinteraction with the nanopore device.

The method may further include detecting the particular molecule,manipulating the particular molecule's location, and/or processing theparticular molecule with a controller. The method may additionallyinclude regulating the material's position with respect to the nanoporedevice with a first electrode and a second electrode.

The method may further include destroying the particular molecule. Themethod may additionally include using at least one of voltage changes incontrol electrodes and ionic current changes to detect the particularmolecule.

Another example aspect of the invention is an embodiment in which apolymer material may be configured to pass through a nanopore device ina controlled manner based upon its interaction with the nanopore device.The embodiment may include a capture mechanism connected to one end ofthe polymer material, with the capture mechanism configured to catch aparticular type of molecule while ignoring other types of molecules. Theembodiment may also include a controller to detect the particularmolecule and/or manipulate the particular molecule's location.

Another aspect of the invention is an embodiment in which a material maybe configured to pass through a nanopore device in a controlled mannerbased upon its interaction with the nanopore device. The embodiment mayinclude a capture mechanism connected to one end of the material, withthe capture mechanism configured to catch a particular type of moleculewhile ignoring other types of molecules. The embodiment may also includea controller to detect the particular molecule and/or manipulate theparticular molecule's location based upon voltage changes in controlelectrodes and/or ionic current changes.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic block diagram of a nanopore capture system inaccordance with the invention.

FIG. 2 is a flowchart illustrating method aspects according to theinvention.

FIG. 3 is a graphical representation of electronically detecting thecatch with the nanopore capture system of FIG. 1.

FIG. 4 is a graphical representation of processing the catch with thenanopore capture system of FIG. 1.

FIG. 5 is an exemplary embodiment of an engineered polypeptide for amaterial to be used as a “fishing string” for the nanopore capturesystem of FIG. 1.

FIG. 6 is exemplary embodiments of non-biological molecules as materialsor “fishing strings” for the nanopore capture system of FIG. 1.

FIG. 7 is exemplary embodiments of some bait species capable ofmolecular recognition for the nanopore capture system of FIG. 1.

FIGS. 8 a and 8 b is a copolymer having charged moiety for the materialto be used as fishing strings in the nanopore capture system of FIG. 1.

FIG. 9 is a flowchart illustrating another method aspect in accordancewith the invention.

FIG. 10 is a flowchart illustrating method aspects according to themethod of FIG. 9.

FIG. 11 is a flowchart illustrating method aspects according to themethod of FIG. 9.

FIG. 12 is a flowchart illustrating method aspects according to themethod of FIG. 10.

FIG. 13 is a flowchart illustrating method aspects according to themethod of FIG. 9.

DETAILED DESCRIPTION

Example embodiments of the invention will now be described more fullyhereinafter with reference to the accompanying drawings, in whichpreferred embodiments of the invention are shown. Like numbers refer tolike elements throughout, like numbers with letter suffixes are used toidentify similar parts in a single embodiment, and letter suffix lowercase n is a variable that indicates an unlimited number of similarelements.

With reference now to FIG. 1, a nanopore capture system 100 is initiallydescribed. According to one embodiment of the invention, the system 100includes a material 115 configured to pass through a nanopore device 101in a controlled manner based upon its interaction with the nanoporedevice. The system 100 also includes a capture mechanism 121 connectedto one end of the material 115. In one embodiment, the capture mechanism121 is configured to catch a particular type of molecule 123 whileignoring other types of molecules 125.

In one embodiment, the material 115 includes a polymer and/or anon-biological molecule. In another embodiment, the polymer comprises apolypeptide.

In one embodiment, the system 100 includes a controller 113 to detectthe particular molecule 123 and/or manipulate the particular molecule'slocation. In another embodiment, the controller 113 detects theparticular molecule 123 based upon voltage changes in control electrodes111 a-111 n and/or ionic current changes.

In one embodiment, the capture mechanism 121 includes an antibody, adeoxyribonucleic acid binding protein, an oligonucleotide, an aptamerand/or nucleic acid fragments for complementary strand hybridization. Inanother embodiment, the controller 113 processes the particular molecule123. The detail description begins with introducing all the elements inrelation to the drawings. Then the detail description discloses the nutsand bolts of the functionality of the invention.

For example, the controller 113 processes the particular molecule 123 bydestroying the particular molecule. In one embodiment, the system 100includes a CIS reservoir 105 adjacent one side of the nanopore device101 that is flushed after the particular molecule 123 is destroyed.

In one embodiment, the system 100 includes a first electrode 127adjacent one side of the nanopore device 101, and a second electrode 129adjacent the other side of the nanopore device. In another embodiment,the first electrode 127 and the second electrode 129 are configured toregulate the material's 115 position with respect to the nanopore device101.

In one embodiment, FIG. 1 illustrates the nanopore device 101 or stator(stationary part) of a single-molecule linear motor situated inside asolid state membrane 103 separating a CIS reservoir 105 and a TRANSreservoir 107. The nanopore device 101 consists of a nanopore 109 andseveral control electrodes 111 a-111 n.

In one embodiment, the controller 113 is capable of applying voltages tocontrol electrodes 111 a-111 n as well as measuring voltages induced inthese electrodes. The controller 113 can be integrated in or near themembrane 103 or can stand alone.

In one embodiment, the material 115 or armature (moving part) of thelinear motor is a single molecule of charged linear polymer. In anotherembodiment, the thick segments 117 a-117 n represent charges on thepolymer chain and thin segments 119 a-119 n represent neutral parts ofthe chain. In addition, as described in U.S. Patent Publication No.2008/0187915, the nanopore device 101 can control the position of thematerial 115 along the longitude axis of nanopore 109 with resolutionbetter than the distance between charges in the polymer chain.Additionally, the nanopore device can position the material 115 bystopping its passage through the nanopore 109, locking this stoppedposition for a period of time, and then start the material 115 movingagain through the nanopore 109.

In one embodiment, one end of material 115 is functionalized with acatching mechanism 121, e.g. a molecule, which is capable of molecularrecognition of other molecular species such as particular molecule 123.In another embodiment, molecular recognition refers to specificinteraction between these two molecules through non-covalent bonding. Inanother embodiment, all other molecular species, such as molecule 125,different from particular molecule 123, do not bind to catchingmechanism 121.

In one embodiment, when particular molecule 123 binds to catchingmechanism 121, the nanopore device 101, e.g. stator, controlled bycontroller 113, is capable of moving particular molecule 123 andanything else that can, in turn, be attached to it. For example, thiscan be a virus, a cell, fragment of a cell, and/or the like. Using afishing analogy, the material 115 can be thought of as “fishing string”,the catching mechanism 121 as “bait”, and the particular molecule 123 asa “catch” or “prey.”

In one embodiment, the system 100 can have multiple nanopores 109 thatcan share a single controller 113. In another embodiment, multiplecontrollers 113 can connect to multiple nanopores 109.

In one embodiment, a drag electrode 127 located in CIS reservoir 127 anda drag electrode 129 located in TRANS reservoir 107, and not inside thenanopore 109, apply a voltage difference between the CIS reservoir andthe TRANS reservoir to attract fishing strings, e.g. material 115,inside the nanopore 109. In another embodiment, the voltage at the dragelectrodes 127 and 129 is set by controller 113.

With additional reference to the block diagram of FIG. 2, the operationof one embodiment of system 100 is outlined. The fishing strings 115with bait 121 are flown in (loaded into) CIS reservoir 105 and loaded(pulled into) in nanopores 109 by a voltage difference between dragelectrodes 127 and 129 at Block 201. Once the fishing strings 115 residein the nanopores 109, the catch 123 and, possibly, other molecularspecies are flown through the CIS reservoir 105 at Block 203.

It is noted that steps 201 and 203 should not necessary be sequential.In fact, the steps 201 and 203 can overlap or even occur simultaneously.

In one embodiment, the binding of a catch 123 is detected electronicallyat Block 205. For example, if the catch 123 is large enough, the viscousdrag applied by the liquid flow on the catch can overcome the electricforce that keeps the fishing string 115 inside the nanopore 109 asillustrated in FIG. 3.

In one embodiment, such an event can be detected when the ionic current301 between the drag electrodes 127 and 129, and/or control electrodes111 a-111 n changes at step 303, returning to the level before thefishing string 115 was loaded at step 305.

In another embodiment, when the catch 123 starts to pull the fishingstring 115 out of the nanopore 109, its charges pass by controlelectrodes 111 a-111 n and induce transient voltage pulses 307. Thecontroller 113 detects such a pulse and, optionally, adjusts thevoltages applied to the linear motor to keep the fishing string 115inside the nanopore 109.

It is noted that not each catch 123 species can be detectedelectronically. In other cases, the detection of catch 123 is notneeded. The optional character of this step is indicated by the dashedline of Block 205.

Also optional is the next step—processing of the catch 123 at Block 207.In one embodiment, illustrated in FIG. 4, the catch is a pathogen, e.g.particular molecule 123, slated for destruction. Once the catch 123binding is detected, the stator 101 pulls the fishing string 115 insidethe nanopore 109, as indicated by arrow 403, and brings the catch in thevicinity of electrodes 111 g and 111 h. The voltage pulse 409 ofsufficient amplitude destroys the pathogen.

In one embodiment, Block 209 of the described procedure is flushing theCIS reservoir 105 so that the unbound catch 123 and any other molecularspecies 125 are removed. In another embodiment, this guarantees thatwhen the controller 113 releases the fishing strings 115, only the catch123 is present downstream for subsequent processing. The above processat Blocks 201, 203, 205, 207, and 209 can be repeated at Block 211.

In one embodiment, a variety of charged polymer molecules can be used asfishing strings 115. For example, one possible embodiment usesengineered polypeptides. FIG. 5 shows a polypeptide fishing string 115consisting of K segments.

In one embodiment, each segment 703 consists of a block 709 of N chargedamino acid residues A 705 and a block 711 of M uncharged amino acidresidues B 707. In another embodiment, charged residues can be lysine,arginine, histidine, and/or the like that are positively charged, oraspartate, glutamate, and/or the like that are negatively charged. Inanother embodiment, uncharged residues can be polar serine, threonine,cysteine, asparagine, glutamine, and/or the like.

In one embodiment, the choice is determined by their hydrophilicitywhich would prevent the polypeptide from forming a tertiary structure,an undesirable feature for a fishing string 115. In another embodiment,the residues in each block do not need to be of same type. In anotherembodiment, the system 100 emphasizes the importance of large blocksizes N and M for practical applications because larger distance betweencharges relaxes requirements on the separation between controlelectrodes of the stator and their thickness, making the linear motoreasier to manufacture.

Another fishing string embodiment is a synthetic polymer consisting ofrepeating units of charged and uncharged moieties. FIG. 6 illustratesthe general structures of this synthetic polymer in which segment 600and 601 are the end groups of the polymer which can be attached to thebait species. The end group 600 and 601 could be the same or different.Segment 620 is the uncharged moiety and segment 630 is the charged. Asexamples of each segment, the end groups 600 and 601 can be chosen fromfunctionalities like hydroxyl (OH), carboxylic (—CO2H), or amine (—NH2),and/or the like functionality. The uncharged segment 620 can be longchain alkyl, alkoxy like polyethyleneoxide, and/or the like, and thecharged segment is represented by conjugated aromatic chains likeoligothiophenes, oligopyrrole, oligoaniline, and/or the like, all ofwhich can be doped with a variety of reagents and acquire electricalcharges.

In one embodiment, the fishing string 115 presents a variety of baitspecies. FIG. 7 outlines some bait species 901 capable of molecularrecognition. Antibody-based bait 903 can identify and bind toantigens—viruses and bacteria. Nucleic acid binding protein baits 905can, possibly specifically, attach to single or double stranded DNAmolecules, RNA molecules, and/or the like.

In one embodiment, for a polypeptide-based fishing string 115, differentdomains of a single protein can serve as a fishing string and bait 121simultaneously, simplifying the manufacturing. In another embodiment,single strands of nucleic acids can be used as bait 907 to catchcomplementary strands by sequence specific hybridization.

In one embodiment, covalent bonds between DNA and protein can be formedenabling robust connection between the fishing string 115 and the bait123. In another embodiment illustrated in FIGS. 8 a and 8 b, a copolymerhaving charged moiety is shown.

Another aspect of the invention is a nanopore capture system method,which is now described with reference to flowchart 20 of FIG. 9. Themethod begins at Block 22 and may include connecting a capture mechanismto one end of a material, with the capture mechanism configured to catcha particular type of molecule while ignoring other types of molecules atBlock 24. The method may also include controlling the passage of thematerial through a nanopore device based upon the material's interactionwith the nanopore device at Block 26. The method ends at Block 28.

In another method embodiment, which is now described with reference toflowchart 30 of FIG. 10, the method begins at Block 32. The method mayinclude the steps of FIG. 9 at Blocks 24 and 26. The method mayadditionally include detecting the particular molecule, manipulating theparticular molecule's location, and/or processing the particularmolecule with a controller at Block 34. The method ends at Block 36.

In another method embodiment, which is now described with reference toflowchart 38 of FIG. 11, the method begins at Block 40. The method mayinclude the steps of FIG. 9 at Blocks 24 and 26. The method mayadditionally include regulating the material's position with respect tothe nanopore device with a first electrode and a second electrode atBlock 42. The method ends at Block 44.

In another method embodiment, which is now described with reference toflowchart 46 of FIG. 12, the method begins at Block 48. The method mayinclude the steps of FIG. 10 at Blocks 24, 26, and 34. The method mayadditionally include destroying the particular molecule at Block 50. Themethod ends at Block 52.

In another method embodiment, which is now described with reference toflowchart 54 of FIG. 13, the method begins at Block 56. The method mayinclude the steps of FIG. 9 at Blocks 24 and 26. The method mayadditionally include using at least one of voltage changes in controlelectrodes and ionic current changes to detect the particular moleculeat Block 58. The method ends at Block 60.

Another aspect of the invention is an embodiment in which a polymermaterial 115 is configured to pass through a nanopore device 101 in acontrolled manner based upon its interaction with the nanopore device.The embodiment includes a capture mechanism 121 connected to one end ofthe polymer material 115, with the capture mechanism configured to catcha particular type of molecule 123, while ignoring other types ofmolecules 125. The embodiment also includes a controller 113 to detectthe particular molecule 123 and/or manipulate the particular molecule'slocation.

Another aspect of the invention is an embodiment in which a material 115is configured to pass through a nanopore device 101 in a controlledmanner based upon its interaction with the nanopore device. Theembodiment includes a capture mechanism 121 connected to one end of thematerial 115, with the capture mechanism configured to catch aparticular type of molecule 123 while ignoring other types of molecules125. The embodiment also includes a controller 113 to detect theparticular molecule 123 and/or manipulate the particular molecule'slocation based upon voltage changes in control electrodes 111 a-111 nand/or ionic current changes.

In view of the foregoing, the system 100 provides a nanopore capturesystem where the fishing line polymer 115 is functionalized with a“bait” 121 that is capable of molecular recognition of other molecularspecies 123 (“catch”). As a result, molecules 123 that do not havelocalized charges periodically located along its chain can bemanipulated using the nanopore capture system 100.

It should be noted that in some alternative implementations, thefunctions noted in a flowchart block may occur out of the order noted inthe figures. For instance, two blocks shown in succession may, in fact,be executed substantially concurrently, or the blocks may sometimes beexecuted in the reverse order, depending upon the functionality involvedbecause the flow diagrams depicted herein are just examples. There maybe many variations to these diagrams or the steps (or operations)described therein without departing from the spirit of the invention.For example, the steps may be performed concurrently and/or in adifferent order, or steps may be added, deleted, and/or modified. All ofthese variations are considered a part of the claimed invention.

Furthermore, the use of the terms a, an, etc. do not denote a limitationof quantity, but rather denote the presence of at least one of thereferenced item. The terminology used herein is for the purpose ofdescribing particular embodiments only and is not intended to belimiting of the invention. As used herein, the singular forms “a”, “an”and “the” are intended to include the plural forms as well, unless thecontext clearly indicates otherwise. It will be further understood thatthe terms “includes” and/or “including,” when used in thisspecification, specify the presence of stated features, integers, steps,operations, elements, and/or components, but do not preclude thepresence or addition of one or more other features, integers, steps,operations, elements, components, and/or groups thereof.

While the preferred embodiment to the invention has been described, itwill be understood that those skilled in the art, both now and in thefuture, may make various improvements and enhancements which fall withinthe scope of the claims which follow. These claims should be construedto maintain the proper protection for the invention first described.

1. A system comprising: a material configured to traverse a nanopore ina solid state membrane device in a controlled manner based upon itsinteraction with the solid state membrane device; and a capturemechanism connected to one end of the material, the capture mechanismconfigured to bond to a particular type of molecule while not bonding toother types of molecules.
 2. The system of claim 1 wherein the materialcomprises at least one of a polymer and a non-biological molecule. 3.The system of claim 2 wherein the polymer comprises one of a polypeptideand an polynucleotide.
 4. The system of claim 1 further comprising acontroller to at least one of detect the particular molecule andmanipulate the particular molecule's location.
 5. The system of claim 1wherein the capture mechanism comprises at least one of an antibody, adeoxyribonucleic acid binding protein, an oligonucleotide, an aptamer,and nucleic acid fragments for complementary strand hybridization. 6.The system of claim 4 wherein the controller processes the particularmolecule.
 7. The system of claim 1 further comprising: a first electrodeadjacent one side of the nanopore device; a second electrode adjacentthe other side of the nanopore device, and the first electrode and thesecond electrode are configured to regulate the material's position withrespect to the nanopore device.
 8. The system of claim 6 wherein thecontroller destroys the particular molecule.
 9. The system of claim 8further comprising a CIS reservoir adjacent one side of the nanoporedevice that is flushed after the particular molecule is destroyed. 10.The system of claim 4 wherein the controller detects the particularmolecule based upon at least one of voltage changes in controlelectrodes and ionic current changes.
 11. A method comprising:connecting a capture mechanism to one end of a material, the capturemechanism configured to catch a particular type of molecule whileignoring other types of molecules; and controlling the passage of thematerial through a nanopore device based upon the material's interactionwith the nanopore device.
 12. The method of claim 11 further comprisingat least one of detecting the particular molecule, manipulating theparticular molecule's location, and processing the particular moleculewith a controller.
 13. The method of claim 11 further comprisingregulating the material's position with respect to the nanopore devicewith a first electrode and a second electrode.
 14. The method of claim12 further comprising destroying the particular molecule.
 15. The methodof claim 11 further comprising using at least one of voltage changes incontrol electrodes and ionic current changes to detect the particularmolecule.
 16. A system comprising: a polymer material configured to passthrough a nanopore device in a controlled manner based upon itsinteraction with the nanopore device; a capture mechanism connected toone end of the polymer material, the capture mechanism configured tocatch a particular type of molecule while ignoring other types ofmolecules; and a controller to at least one of detect the particularmolecule and manipulate the particular molecule's location.
 17. Thesystem of claim 16 wherein the polymer material comprises one of apolypeptide and a polynucleotide.
 18. The system of claim 16 wherein thecapture mechanism comprises at least one of an antibody, adeoxyribonucleic acid binding protein, an oligonucleotide, an aptamerand nucleic acid fragments for complementary strand hybridization. 19.The system of claim 16 wherein the controller processes the particularmolecule.
 20. The system of claim 16 further comprising: a firstelectrode adjacent one side of the nanopore device; a second electrodeadjacent the other side of the nanopore device, and the first electrodeand the second electrode are configured to regulate the polymermaterial's position with respect to the nanopore device.
 21. The systemof claim 16 wherein the controller destroys the particular molecule. 22.The system of claim 21 further comprising a CIS reservoir adjacent oneside of the nanopore device that is flushed after the particularmolecule is destroyed.
 23. The system of claim 16 wherein the controllerdetects the particular molecule based upon at least one of voltagechanges in control electrodes and ionic current changes.
 24. A systemcomprising: a material configured to pass through a nanopore device in acontrolled manner based upon its interaction with the nanopore device; acapture mechanism connected to one end of the material, the capturemechanism configured to catch a particular type of molecule whileignoring other types of molecules; and a controller to at least one ofdetect the particular molecule and manipulate the particular molecule'slocation based upon at least one of voltage changes in controlelectrodes and ionic current changes.
 25. The system of claim 24 furthercomprising: a first electrode adjacent one side of the nanopore device;a second electrode adjacent the other side of the nanopore device, andthe first electrode and the second electrode are configured to regulatethe material's position with respect to the nanopore device.